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    TMEM39B transmembrane protein 39B [ Homo sapiens (human) ]

    Gene ID: 55116, updated on 3-Apr-2024

    Summary

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    Official Symbol
    TMEM39Bprovided by HGNC
    Official Full Name
    transmembrane protein 39Bprovided by HGNC
    Primary source
    HGNC:HGNC:25510
    See related
    Ensembl:ENSG00000121775 AllianceGenome:HGNC:25510
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be integral component of membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in placenta (RPKM 2.8), testis (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p35.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32072031..32102863)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (31929980..31960816)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (32537632..32568464)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC128031832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32389035-32389578 Neighboring gene protein tyrosine phosphatase 4A2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 659 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 660 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:32403472-32403643 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 581 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 661 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32409768-32410302 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32419864-32420642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32420643-32421419 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32421420-32422197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 667 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:32473819-32474378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32479704-32480274 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 583 Neighboring gene KH RNA binding domain containing, signal transduction associated 1 Neighboring gene VISTA enhancer hs645 Neighboring gene NANOG hESC enhancer GRCh37_chr1:32526442-32527054 Neighboring gene Sharpr-MPRA regulatory region 15509 Neighboring gene Sharpr-MPRA regulatory region 7843 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32532900-32533694 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32537939-32538544 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:32557367-32557892 Neighboring gene microRNA 5585 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32573351-32573869 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32573870-32574387 Neighboring gene Sharpr-MPRA regulatory region 5670 Neighboring gene karyopherin subunit alpha 6 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:32644454-32645213 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:32645214-32645972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 671 Neighboring gene taxilin alpha Neighboring gene coiled-coil domain containing 28B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl A, et al. Nature, 2011 Dec 1. PMID 22020285, Free PMC Article
    2. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Wagner SA, et al. Mol Cell Proteomics, 2011 Oct. PMID 21890473, Free PMC Article
    3. Large-scale analysis of the human ubiquitin-related proteome. Matsumoto M, et al. Proteomics, 2005 Nov. PMID 16196087
    4. Quantitative Lys-ϵ-Gly-Gly (diGly) proteomics coupled with inducible RNAi reveals ubiquitin-mediated proteolysis of DNA damage-inducible transcript 4 (DDIT4) by the E3 ligase HUWE1. Thompson JW, et al. J Biol Chem, 2014 Oct 17. PMID 25147182, Free PMC Article
    5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. Wiemann S, et al. Genome Res, 2001 Mar. PMID 11230166, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10315

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    transmembrane protein 39B

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001319677.2 → NP_001306606.1  transmembrane protein 39B isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon, resulting in a different 5' UTR and use of a downstream in-frame start codon, compared to variant 1. It encodes isoform 2, which is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK091861, AK300293
      UniProtKB/TrEMBL
      B3KRL9, Q9NW51
      Related
      ENST00000487305.5
      Conserved Domains (1) summary
      pfam10271
      Location:1 → 351
      Tmp39; Putative transmembrane protein

    2. NM_001319678.2 → NP_001306607.1  transmembrane protein 39B isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK298766, AL136695, DA614559
      UniProtKB/TrEMBL
      B3KRL9
      Conserved Domains (1) summary
      pfam10271
      Location:1 → 279
      Tmp39; Putative transmembrane protein

    3. NM_001319679.2 → NP_001306608.1  transmembrane protein 39B isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream in-frame start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      BC004364, DA614559
      UniProtKB/TrEMBL
      B3KRL9
      Conserved Domains (1) summary
      pfam10271
      Location:1 → 279
      Tmp39; Putative transmembrane protein

    4. NM_018056.4 → NP_060526.2  transmembrane protein 39B isoform 1

      See identical proteins and their annotated locations for NP_060526.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK023331, BC004364
      Consensus CDS
      CCDS351.2
      UniProtKB/Swiss-Prot
      B4DKN8, B4DQE6, B4DTN8, D3DPP4, Q6IA44, Q9GZU3
      Related
      ENSP00000338165.5, ENST00000336294.10
      Conserved Domains (1) summary
      pfam10271
      Location:51 → 478
      Tmp39; Putative transmembrane protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32072031..32102863
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423840.1 → XP_047279796.1  transmembrane protein 39B isoform X1

    2. XM_006710725.5 → XP_006710788.1  transmembrane protein 39B isoform X3

      See identical proteins and their annotated locations for XP_006710788.1

      Conserved Domains (1) summary
      pfam10271
      Location:51 → 414
      Tmp39; Putative transmembrane protein

    3. XM_006710724.3 → XP_006710787.1  transmembrane protein 39B isoform X2

      Conserved Domains (1) summary
      pfam10271
      Location:51 → 414
      Tmp39; Putative transmembrane protein

    4. XM_047423846.1 → XP_047279802.1  transmembrane protein 39B isoform X4

    5. XM_047423842.1 → XP_047279798.1  transmembrane protein 39B isoform X4

    6. XM_005270988.3 → XP_005271045.1  transmembrane protein 39B isoform X6

      See identical proteins and their annotated locations for XP_005271045.1

      UniProtKB/TrEMBL
      B3KRL9, Q9NW51
      Conserved Domains (1) summary
      pfam10271
      Location:1 → 351
      Tmp39; Putative transmembrane protein

    7. XM_047423852.1 → XP_047279808.1  transmembrane protein 39B isoform X8

    8. XM_011541683.2 → XP_011539985.1  transmembrane protein 39B isoform X6

      See identical proteins and their annotated locations for XP_011539985.1

      UniProtKB/TrEMBL
      B3KRL9, Q9NW51
      Conserved Domains (1) summary
      pfam10271
      Location:1 → 351
      Tmp39; Putative transmembrane protein

    9. XM_017001595.2 → XP_016857084.1  transmembrane protein 39B isoform X5

      UniProtKB/TrEMBL
      B3KRL9
      Conserved Domains (1) summary
      pfam10271
      Location:3 → 363
      Tmp39; Putative transmembrane protein

    10. XM_047423851.1 → XP_047279807.1  transmembrane protein 39B isoform X7

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      31929980..31960816
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337330.1 → XP_054193305.1  transmembrane protein 39B isoform X1

    2. XM_054337332.1 → XP_054193307.1  transmembrane protein 39B isoform X3

    3. XM_054337331.1 → XP_054193306.1  transmembrane protein 39B isoform X2

    4. XM_054337334.1 → XP_054193309.1  transmembrane protein 39B isoform X4

    5. XM_054337333.1 → XP_054193308.1  transmembrane protein 39B isoform X4

    6. XM_054337336.1 → XP_054193311.1  transmembrane protein 39B isoform X6

      UniProtKB/TrEMBL
      Q9NW51

    7. XM_054337339.1 → XP_054193314.1  transmembrane protein 39B isoform X8

    8. XM_054337337.1 → XP_054193312.1  transmembrane protein 39B isoform X6

      UniProtKB/TrEMBL
      Q9NW51

    9. XM_054337335.1 → XP_054193310.1  transmembrane protein 39B isoform X5

    10. XM_054337338.1 → XP_054193313.1  transmembrane protein 39B isoform X7

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9GZU3.1 GenPept UniProtKB/Swiss-Prot:Q9GZU3

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